Locus 3723

Sequence ID 2L_DroMel_CAF1
Location 10,848,200 – 10,848,339
Length 139
Max. P 0.969605
window5862 window5863 window5864

overview

Window 2

Location 10,848,200 – 10,848,299
Length 99
Sequences 6
Columns 100
Reading direction forward
Mean pairwise identity 79.20
Mean single sequence MFE -30.33
Consensus MFE -23.86
Energy contribution -23.33
Covariance contribution -0.53
Combinations/Pair 1.15
Mean z-score -2.75
Structure conservation index 0.79
SVM decision value 1.64
SVM RNA-class probability 0.969605
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10848200 99 + 22407834
AUUGAUUUCAUUUGCCAUGCGUGGCAAUUGCA-AUACUUACACAGCUGUGUGCAGAACAAAGUCCUUGGUGGUGUAGCCAAGGGCAAAGUUGUUGGUGGU
........((.((((((....)))))).))..-.((((...((((((.(((.....)))..(((((((((......)))))))))..)))))).)))).. ( -32.20)
>DroGri_CAF1 99541 89 + 1
AUAGAGUUU----GUAAUAC-UG-----UGU-AUUACUUACACGGCUGUGUGCAGGACAAAGUCCUUGGCGGAGUAGCCGAGGGCAAAGUUGUUGGUGGU
.......((----(((((((-((-----(((-(.....))))))).))).)))))(((((.(((((((((......)))))))))....)))))...... ( -31.20)
>DroEre_CAF1 82552 96 + 1
AUUGAUUUAA---ACCAAGUGUGCCAGAUGUA-AUACUUACACAGCUGUGUGCAGAACAAAGUCCUUGGUGGUGUAGCCAAGGGCAAAGUUGUUGGUGGU
..........---((((..((..((((.((((-.....))))...))).)..)).(((((.(((((((((......)))))))))....)))))..)))) ( -29.90)
>DroWil_CAF1 130024 94 + 1
GGAAAUUUCA---AGCAGGACUAACAAAA---UUUACUUACACAGCUGUGUGCAGGACAAAGUCCUUGGUGGUAUAGCCAAGGGCAAAGUUGUUGGUGGU
..........---......((((((((..---....(((((((....))))).))......(((((((((......)))))))))....))))))))... ( -28.50)
>DroYak_CAF1 84435 93 + 1
AUUGAUUUUU---GCCAAGUGUGCCAGGUGU----ACUUACACAGCUGUGUGCAGAACAAAGUCCUUGGUGGUGUAGCCAAGGGCAAAGUUGUUGGUGGU
........(.---.((...((..((((.(((----......))).))).)..)).(((((.(((((((((......)))))))))....)))))))..). ( -33.40)
>DroAna_CAF1 93009 90 + 1
AUUAAAAGGA---ACAAUGAG-----AGUG-G-UUACUUACACAGCUGUGUGCAGGACAAAGUCCUUGGUGGUGUAGCCAAGGGCAAAGUUGUUGGUGGU
.....(((.(---((.((...-----.)).-)-)).))).(((..(((....)))(((((.(((((((((......)))))))))....))))).))).. ( -26.80)
>consensus
AUUGAUUUCA___ACCAUGAGUG_CAAAUGU__UUACUUACACAGCUGUGUGCAGAACAAAGUCCUUGGUGGUGUAGCCAAGGGCAAAGUUGUUGGUGGU
........................................(((..(((....)))(((((.(((((((((......)))))))))....))))).))).. (-23.86 = -23.33 +  -0.53)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 10,848,200 – 10,848,299
Length 99
Sequences 6
Columns 100
Reading direction reverse
Mean pairwise identity 79.20
Mean single sequence MFE -19.55
Consensus MFE -12.70
Energy contribution -12.87
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.14
Structure conservation index 0.65
SVM decision value 1.13
SVM RNA-class probability 0.920353
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10848200 99 - 22407834
ACCACCAACAACUUUGCCCUUGGCUACACCACCAAGGACUUUGUUCUGCACACAGCUGUGUAAGUAU-UGCAAUUGCCACGCAUGGCAAAUGAAAUCAAU
.............((((((((((........)))))).........((((((....)))))).....-.))))((((((....))))))........... ( -23.30)
>DroGri_CAF1 99541 89 - 1
ACCACCAACAACUUUGCCCUCGGCUACUCCGCCAAGGACUUUGUCCUGCACACAGCCGUGUAAGUAAU-ACA-----CA-GUAUUAC----AAACUCUAU
.............((((...(((((.....((..(((((...)))))))....))))).))))(((((-((.-----..-)))))))----......... ( -20.10)
>DroEre_CAF1 82552 96 - 1
ACCACCAACAACUUUGCCCUUGGCUACACCACCAAGGACUUUGUUCUGCACACAGCUGUGUAAGUAU-UACAUCUGGCACACUUGGU---UUAAAUCAAU
...(((((......(((((((((........))))).....(((..(((((((....))))..))).-.)))...))))...)))))---.......... ( -19.50)
>DroWil_CAF1 130024 94 - 1
ACCACCAACAACUUUGCCCUUGGCUAUACCACCAAGGACUUUGUCCUGCACACAGCUGUGUAAGUAAA---UUUUGUUAGUCCUGCU---UGAAAUUUCC
...((.(((((.(((((((((((........)))))).........((((((....)))))).)))))---..))))).))......---.......... ( -18.60)
>DroYak_CAF1 84435 93 - 1
ACCACCAACAACUUUGCCCUUGGCUACACCACCAAGGACUUUGUUCUGCACACAGCUGUGUAAGU----ACACCUGGCACACUUGGC---AAAAAUCAAU
............(((((((((((........))))))...............(((.(((((.((.----....)).))))).)))))---)))....... ( -20.00)
>DroAna_CAF1 93009 90 - 1
ACCACCAACAACUUUGCCCUUGGCUACACCACCAAGGACUUUGUCCUGCACACAGCUGUGUAAGUAA-C-CACU-----CUCAUUGU---UCCUUUUAAU
.........(((..((....(((.(((.......(((((...)))))(((((....)))))..))).-)-))..-----..))..))---)......... ( -15.80)
>consensus
ACCACCAACAACUUUGCCCUUGGCUACACCACCAAGGACUUUGUCCUGCACACAGCUGUGUAAGUAA__ACACUUG_CACACAUGGC___UAAAAUCAAU
.................((((((........)))))).........(((((......)))))...................................... (-12.70 = -12.87 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 10,848,227 – 10,848,339
Length 112
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 83.96
Mean single sequence MFE -38.90
Consensus MFE -30.96
Energy contribution -30.27
Covariance contribution -0.69
Combinations/Pair 1.29
Mean z-score -2.00
Structure conservation index 0.80
SVM decision value 0.46
SVM RNA-class probability 0.744628
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10848227 112 + 22407834
-UUGCA-----AUACUUACACAGCUGUGUGCAGAACAAAGUCCUUGGUGGUGUAGCCAAGGGCAAAGUUGUUGGUGGUCAGCUUGGACUGUUGUGUGUCAAAUGCGGUCUGGUAGCCG
-..(((-----.....((((((((...((.(........(((((((((......))))))))).((((((........))))))).)).)))))))).....)))(((......))). ( -38.40)
>DroVir_CAF1 113949 115 + 1
--CUG-AUUGUUUACUUACACGGCUGUGUGGAGGACAAAGUCCUUGGUGGAGUAGCCGAGGGCAAAGUUGUUGGUGGUCAACUUGGACUGUUGUGUAUCGAAUGCGGUCUGAUAACCG
--..(-(((((.....((((((((.((.(..........(((((((((......))))))))).((((((........))))))).)).))))))))......))))))......... ( -36.30)
>DroGri_CAF1 99559 111 + 1
--UGU-----AUUACUUACACGGCUGUGUGCAGGACAAAGUCCUUGGCGGAGUAGCCGAGGGCAAAGUUGUUGGUGGUCAACUUGGACUGUUUUGUAUCGAAUGCGGUCUGAUAGCCG
--(((-----(.....))))(((((((((((((((((..(((((((((......))))))))).((((((........))))))....))))))))))((....)).....))))))) ( -42.10)
>DroWil_CAF1 130048 110 + 1
-AA-------UUUACUUACACAGCUGUGUGCAGGACAAAGUCCUUGGUGGUAUAGCCAAGGGCAAAGUUGUUGGUGGUCAACUUGGCUUUCUGUGUAUCGAAUGCCGUCUGGUAGCCA
-..-------.((((((((((....)))))..((((...(((((((((......))))))))).((((((........))))))(((.(((........))).))))))))))))... ( -36.20)
>DroMoj_CAF1 117162 115 + 1
--ACG-AAUUUGUACUUACACGGCUGUGUGCAGGACAAAGUCCUUGGUGGAGUAGCCGAGGGCAAAGUUGUUGGUGGUCAACUUGGAUUGUUGUGUAUCGAAGGCAGUUUGAUAGCCA
--...-...............(((((((((((.(((((.(((((((((......))))))))).((((((........))))))...))))).)))))((((.....)))))))))). ( -38.10)
>DroPer_CAF1 82492 118 + 1
GGUGCUACUGUUUACUUACACAGAUGUGUGCAAGACAAAGUCCUUGGUGGUGUAGCCAAGGGCAAAGUUGUUGGUGGUCAACUUGGUCUGUUGCGUAUCAAAUGCGGCCUGGUAGCCG
.(.((((((.......(((((....)))))..((((...(((((((((......))))))))).((((((........)))))).))))(((((((.....)))))))..))))))). ( -42.30)
>consensus
__UGC_____UUUACUUACACAGCUGUGUGCAGGACAAAGUCCUUGGUGGAGUAGCCAAGGGCAAAGUUGUUGGUGGUCAACUUGGACUGUUGUGUAUCGAAUGCGGUCUGAUAGCCG
..............(((((((....))))).))(((((.(((((((((......)))))))))....)))))...(((....(..((((((............))))))..)..))). (-30.96 = -30.27 +  -0.69)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:27 2006